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- PDB-6exd: Crystal structure of DotM cytoplasmic domain (residues 153-380) S... -

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Basic information

Entry
Database: PDB / ID: 6exd
TitleCrystal structure of DotM cytoplasmic domain (residues 153-380) SeMet derivative
ComponentsIcmP (DotM)
KeywordsPROTEIN BINDING / Membrane protein / secretion system / type 4 secretion system / Legionella pneumophila
Function / homology: / DotM, C-terminal cytoplasmic domain / : / protein transport / plasma membrane / Type 4 apparatus protein DotM
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsMeir, A. / Waksman, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council321630 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Legionella DotM structure reveals a role in effector recruiting to the Type 4B secretion system.
Authors: Meir, A. / Chetrit, D. / Liu, L. / Roy, C.R. / Waksman, G.
History
DepositionNov 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IcmP (DotM)
B: IcmP (DotM)


Theoretical massNumber of molelcules
Total (without water)54,0492
Polymers54,0492
Non-polymers00
Water2,360131
1
A: IcmP (DotM)

B: IcmP (DotM)


Theoretical massNumber of molelcules
Total (without water)54,0492
Polymers54,0492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455y-1,-x+y,z+1/61
Buried area1700 Å2
ΔGint-16 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.000, 118.000, 66.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein IcmP (DotM)


Mass: 27024.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Gene: icmP, lpg0445 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BLR / References: UniProt: Q5ZYC7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.0 0.15 M NH4SO4 25 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.14→50.01 Å / Num. obs: 29190 / % possible obs: 99.5 % / Redundancy: 13.2 % / CC1/2: 0.97 / Rsym value: 0.253 / Net I/σ(I): 9.11
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.415 / Rsym value: 1.137 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→50.01 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.548 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22749 1469 5 %RANDOM
Rwork0.1913 ---
obs0.19303 27700 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.303 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.41 Å20 Å2
2--0.81 Å20 Å2
3----2.64 Å2
Refinement stepCycle: 1 / Resolution: 2.14→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 0 131 3627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193594
X-RAY DIFFRACTIONr_bond_other_d0.0030.023504
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.9864856
X-RAY DIFFRACTIONr_angle_other_deg1.15838043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8245434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37222.781169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.45915582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2061539
X-RAY DIFFRACTIONr_chiral_restr0.1150.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213999
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02828
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.722.7551742
X-RAY DIFFRACTIONr_mcbond_other2.7182.7541741
X-RAY DIFFRACTIONr_mcangle_it4.3614.1072174
X-RAY DIFFRACTIONr_mcangle_other4.3614.1082175
X-RAY DIFFRACTIONr_scbond_it4.1143.3581852
X-RAY DIFFRACTIONr_scbond_other4.1073.3541850
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4064.8052682
X-RAY DIFFRACTIONr_long_range_B_refined8.522.6824350
X-RAY DIFFRACTIONr_long_range_B_other8.4922.6474319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.138→2.193 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 112 -
Rwork0.302 1935 -
obs--94.38 %

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